Site Number | Classification | USGS Site ID | Site Name | Sampling Date (1997) | Drainage Basin Area (sq.miles) |
| 01 | URB | 01304500 | Peconic River at Riverhead | June 12 | 75 |
| 02 | URB | 01309500 | Massapequa Creek at Massapequa | June 16 | 38 |
| 03 | FOR | 04268000 | Raquette River at Raymondville | June 19 | 1130 |
| 04 | LAG | 01372043 | Hudson River near Poughkeepsie | June 09 | 11700 |
| 05 | FOR | 04275500 | Ausable River near Au Sable Forks | June 18 | 448 |
| 06 | URB | 01375000 | Croton River at New Croton Dam near Croton-on-Hudson | June 16 | 378 |
| 07 | URB | 01376500 | Saw Mill River at Yonkers | June 09 | 25.6 |
| 08 | LAG | 01361200 | Claverack Creek at Claverack | June 10 | 60.6 |
| 09 | LAG | 04280450 | Mettawee River near Middle Granville | June 12 | 167 |
| 10 | LAG | 01371500 | Wallkill River at Gardiner | June 16 | 695 |
| 11 | LAG | 01351450 | Schoharie Creek at Esperance | June 11 | 875 |
| 12 | LAG | 01351270 | West Creek near Warnersville | June 10 | 53 |
| 13 | FOR | 01434025 | Biscuit Brook above Pigeon Brook at Frost Valley | June 09 | 3.72 |
| 14 | LAG | 01434000 | Delaware River at Port Jervis | June 17 | 3070 |
| 15 | URB | 01356220 | Stony Creek at Vischer Ferry | June 12 | 12 |
| 16 | LAG | 04260500 | Black River at Watertown | June 19 | 1860 |
| 17 | LAG | 01423000 | West Branch Delaware River at Walton | June 17 | 332 |
| 18 | HAG | 04249000 | Oswego River at Lock 7, Oswego | June 09 | 5100 |
| 19 | LAG | 04247000 | Oneida River near Euclid | June 09 | 1439 |
| 20 | LAG | 03011020 | Allegheny River at Salamance | June 18 | 1610 |
| 21 | LAG | 01513831 | Susquehanna River at Owego | June 10 | 4220 |
| 22 | HAG | 04235000 | Canadaigua Outlet at Chapin | June 16 | 195 |
| 23 | HAG | 04235820 | Grout Brook tributary southeast of Fair Haven | June 17 | 0.27 |
| 24 | HAG | 04235276 | Black Brook at Tyre | June 16 | 19 |
| 25 | HAG | 04235250 | Flint Creek at Phelps | June 11 | 102 |
| 26 | HAG | 04231000 | Black Creek at Churchville | June 16 | 130 |
| 27 | HAG | 01529500 | Cohocton River near Campbell | June 10 | 470 |
| 28 | HAG | 04218000 | Tonawanda Creek at Rapids | June 10 | 349 |
| 29 | HAG | 04216418 | Tonawanda Creek at Attica | June 10 | 76.9 |
| 30 | LAG | 01510000 | Otselic River at Cincinnatus | June 17 | 147 |
| 31 | HAG | 04230500 | Oatka Creek at Garbutt | June 16 | 200 |
| 32 | HAG | 04245200 | Butternut Creek near Jamesville | June 17 | 32.2 |
| 33 | HAG | 04213500 | Cattaraugus Creek at Gowanda | June 18 | 436 |
| 34 | ORV | 04232100 | Sterling Creek at Sterling | June 09 | 44.4 |
| 35 | ORV | 04219650 | Fourmile Creek near Youngstown | June 17 | 19.7 |
| 36 | ORV | 04232070 | Salmon Creek near Sodus | June 16 | 26.0 |
| 37 | ORV | 04232060 | Salmon Creek at Pultneyville | June 16 | 18.1 |
| 38 | ORV | 04219726 | Lake Ontario Tributary No. 150 near Wilson | June 17 | 4.58 |
| 39 | ORV | 423034077092601 | Unnamed tributary to Keuka Lake | June 09 | 0.75 |
| 40 | ORV | 0423241755 | Bullhorn Creek at McGrath Point | June 09 | 1.21 |
| 41 | ORV | 424104077180001 | Unnnamed tributary to Canadaigua Lake | June 09 | 0.25 |
| 42 | ORV | 0421337640 | Beaver Creek near Cordova | June 17 | 4.02 |
| 43 | ORV | 0421332805 | Spring Creek at mouth near Westfield | June 17 | 2.4 |
| 44 | HAG | 423939077465201 | Unnamed stream near Shakers Crossing | June 10 | 17.5 |
| 45 | HAG | 425540078140101 | Unnamed stream near Alexander | June 10 | 0.080 |
| 46 | LAG | 04228915 | Reynolds Brook at Canandice Lake Rd. | June 12 | 3.48 |
| 47 | FOR | 03011505 | Red House Brook south of Red House Lake | June 17 | 3.78 |
| 48 | LAG | 422950076305901 | Cayuga Lake near Bolton Point | July 02 | 786 |
| 49 | LAG | 425549076250201 | Skaneateles Lake near Skaneateles | July 02 | 72.7 |
| 50 | HAG | 424618077364701 | Hemlock Lake near Hemlock | July 02 | 45.4 |
| 51 | HAG | 04229500 | Honeoye Creek at Honeoye Falls | June 11 | 196 |
| 60 | URB | 01304000 | Nissequogue River near Smithtown | June 16 | 27 |
| 61 | URB | 01305000 | Carmans River at Yaphank | June 18 | 71 |
| 62 | URB | 01305500 | Swan River at East Patchogue | June 18 | 8.8 |
| 63 | URB | 01306495 | Connetquot River near Oakdale | June 17 | 24.3 |
| 64 | URB | 01308000 | Sampawams Creek at Babylon | June 17 | 22.7 |
| 65 | URB | 01308500 | Carmans River at Yaphank | June 17 | 35.4 |
| 66 | URB | 01309100 | Santapogue River (Highway 27A) at Linde | June 17 | 5.42 |
| F1 | HAG | 01349150 | Canajoharie Creek near Canajoharie | June 11 | 59.7 |
| F2 | LAG | 01357500 | Mohawk River at Cohoes | June 11 | 3450 |
| F3 | HAG | 04237500 | Seneca River at Baldwinsville | June 11 | 3140 |
| F4 | HAG | 04234000 | Fall Creek near Ithaca | June 11 | 126 |
| F5 | HAG | 04228500 | Genesee River at Avon | June 10 | 1670 |
| F6 | HAG | 04227000 | Canaseraga Creek at Shakers Crossing | June 10 | 335 |